I had a lot of success eating gluten free in Charleston, but it was two - three years ago and I was only a couple weeks into being gluten free, so even though I emailed everyone before I left about gluten free, I still probably had some cross contamination questions I didn't address. I will look for my list (I am a planner) and see where we ate and come back and repost, but off the top of my head i know that they have:

Mellow Mushroom - gluten free pizza - they are a chain and a local celiac told me about this one

Yo Burrito - I emailed in advance and they had many options for gluten free, I will say that their serving sizes were very big and some stuff was a little spicey.

Both this places are downtown. I will see if I can find my trip inoformation and send you more. My suggestion would be to still email them and ask I then take that email and ask to speak to the person who answered me.